1) there is an issue with your settings (this is an old issue) which I fixed in your settings.
- Download the attached file
- open it in a TEXT editor
- copy the contents
- go to ATO->Export/Import->Import Atahualpa settings file
- paste the settings and press the 'Import Settings' button
- go look to see if it is fixed.
I do not think this is your issue, but it needs to be fixed
2) did you check to see if the widgets were in the widget area and not the 'inactive' widget area?
Quote:
WordPress created a new requirement for themes - dealing with widgets - that had to be included in themes or your theme would fail the review and not be approved. And it effects your widgets.
If you go to your widgets page, you should see all your widgets in the 'inactive widgets' area - you can just drag them back to the sidebars.
-- this was taken from a sticky post from back in May of 2015 in the "Installation/Upgrade Issues" forum with the title "Sidebar reset after upgrading to version 3.7.24 "